diff --git a/bims/api_views/taxon.py b/bims/api_views/taxon.py
index 4d781fc9b..c611a973f 100644
--- a/bims/api_views/taxon.py
+++ b/bims/api_views/taxon.py
@@ -5,6 +5,7 @@
from django.contrib.auth import get_user_model
from django.db import transaction, IntegrityError
+from django.forms import model_to_dict
from django.http import Http404
from django.db.models import Count, Case, Value, When, F, CharField, Prefetch, Q
from django.contrib.auth.mixins import LoginRequiredMixin
@@ -358,20 +359,34 @@ def post(self, request, *args):
taxonomy.save()
with transaction.atomic():
- TaxonomyUpdateProposal.objects.get_or_create(
- original_taxonomy=taxonomy,
- taxon_group=taxon_group,
- status='pending',
- new_data=True,
- scientific_name=taxonomy.scientific_name,
- canonical_name=taxonomy.canonical_name,
- rank=taxonomy.rank,
- parent=taxonomy.parent,
- taxonomic_status=taxonomy.taxonomic_status,
- legacy_canonical_name=taxonomy.legacy_canonical_name,
- taxon_group_under_review=taxon_group,
- author=author_name,
+ taxonomy_data = model_to_dict(
+ taxonomy,
+ exclude=[
+ 'id',
+ 'iucn_status',
+ 'vernacular_names',
+ 'author',
+ 'tags',
+ 'biographic_distributions',
+ 'owner',
+ 'parent'])
+ taxonomy_update_proposal, created = (
+ TaxonomyUpdateProposal.objects.get_or_create(
+ original_taxonomy=taxonomy,
+ taxon_group=taxon_group,
+ status='pending',
+ new_data=True,
+ owner=taxonomy.owner,
+ parent=taxonomy.parent,
+ taxon_group_under_review=taxon_group,
+ author=author_name,
+ iucn_status=taxonomy.iucn_status,
+ **taxonomy_data
+ )
)
+ if created:
+ vernacular_names_instances = list(taxonomy.vernacular_names.all())
+ taxonomy_update_proposal.vernacular_names.set(vernacular_names_instances)
return Response(response)
diff --git a/bims/tasks/harvest_gbif_species.py b/bims/tasks/harvest_gbif_species.py
index 0d4120180..d7233f4e1 100644
--- a/bims/tasks/harvest_gbif_species.py
+++ b/bims/tasks/harvest_gbif_species.py
@@ -8,7 +8,6 @@ def harvest_gbif_species(session_id):
from bims.utils.logger import log
from bims.models import HarvestSession
from bims.utils.gbif import find_species_by_area
- from bims.enums import TaxonomicRank
try:
harvest_session = (
@@ -30,7 +29,7 @@ def harvest_gbif_species(session_id):
parent_species = harvest_session.module_group.gbif_parent_species
- taxa = find_species_by_area(
+ find_species_by_area(
harvest_session.boundary_id,
harvest_session=harvest_session,
parent_species=parent_species,
diff --git a/bims/templates/harvest_gbif_species.html b/bims/templates/harvest_gbif_species.html
index bab849a6f..d63e0ab4d 100644
--- a/bims/templates/harvest_gbif_species.html
+++ b/bims/templates/harvest_gbif_species.html
@@ -38,6 +38,15 @@
Harvest GBIF species
+
+ {% if messages %}
+
+ {% for message in messages %}
+
{{ message }}
+ {% endfor %}
+
diff --git a/bims/utils/gbif.py b/bims/utils/gbif.py
index aa874a99b..6b5251b97 100644
--- a/bims/utils/gbif.py
+++ b/bims/utils/gbif.py
@@ -15,7 +15,6 @@
from bims.models.vernacular_name import VernacularName
from bims.enums import TaxonomicRank, TaxonomicStatus
from bims.models.harvest_session import HarvestSession
-from bims.models.boundary import Boundary
logger = logging.getLogger(__name__)
@@ -510,6 +509,7 @@ def add_parent_to_group(taxon: Taxonomy, group: TaxonGroup):
return
def fetch_occurrences_by_area(geometry_string):
+ from bims.scripts.import_gbif_occurrences import API_BASE_URL
facet_offset = 0
while True:
@@ -531,6 +531,22 @@ def fetch_occurrences_by_area(geometry_string):
]
}
+ gbif_url = (
+ f"{API_BASE_URL}?"
+ f"{parent_species.rank.lower()}Key={parent_species.gbif_key}&"
+ f"facet=acceptedTaxonKey&"
+ f"facetLimit=100&"
+ f"facetMinCount=1&"
+ f"hasCoordinate=true&"
+ f"hasGeospatialIssue=false&"
+ f"basisOfRecord=HUMAN_OBSERVATION&"
+ f"limit={0}&"
+ f"geometry={geometry_string}&"
+ f"facetOffset={facet_offset}&"
+ )
+
+ log_info(gbif_url)
+
occurrences_data = search(**params)
log_info(occurrences_data)
except Exception as e:
diff --git a/bims/views/harvest_gbif_species.py b/bims/views/harvest_gbif_species.py
index 2de0c39e6..1edf41c03 100644
--- a/bims/views/harvest_gbif_species.py
+++ b/bims/views/harvest_gbif_species.py
@@ -4,9 +4,10 @@
from datetime import datetime
from django.conf import settings
+from django.contrib import messages
from django.contrib.auth.mixins import UserPassesTestMixin, LoginRequiredMixin
from django.db.models import Q
-from django.http import HttpResponseRedirect
+from django.http import HttpResponseRedirect, Http404
from django.views.generic import TemplateView
from django.core.files import File
from bims.models.taxon_group import TaxonGroup
@@ -72,8 +73,6 @@ def get_context_data(self, **kwargs):
def post(self, request, *args, **kwargs):
taxon_group_id = request.POST.get('taxon_group', None)
- taxon_group_logo = request.FILES.get('taxon_group_logo')
- taxon_group_name = request.POST.get('taxon_group_name', '')
boundary_id = request.POST.get('boundary', None)
cancel = ast.literal_eval(request.POST.get(
'cancel', 'False'
@@ -89,21 +88,25 @@ def post(self, request, *args, **kwargs):
return HttpResponseRedirect(request.path_info)
except (HarvestSession.DoesNotExist, ValueError):
pass
- if taxon_group_logo and taxon_group_logo:
- taxon_groups = TaxonGroup.objects.filter(
- category='SPECIES_MODULE'
- ).order_by('-display_order')
- display_order = 1
- if taxon_groups:
- display_order = taxon_groups[0].display_order + 1
- TaxonGroup.objects.create(
- name=taxon_group_name,
- logo=taxon_group_logo,
- category='SPECIES_MODULE',
- display_order=display_order
- )
+
+ taxon_group = TaxonGroup.objects.get(id=taxon_group_id)
+ if not taxon_group.gbif_parent_species:
+ messages.error(
+ self.request,
+ 'GBIF Species is missing. Please add it on the taxon management page.')
return HttpResponseRedirect(request.path_info)
+ gbif_taxonomy = taxon_group.gbif_parent_species
+ if not gbif_taxonomy.gbif_key:
+ if gbif_taxonomy.gbif_data and 'key' in gbif_taxonomy.gbif_data:
+ gbif_taxonomy.gbif_key = gbif_taxonomy.gbif_data['key']
+ gbif_taxonomy.save()
+ else:
+ messages.error(
+ self.request,
+ f'GBIF key is missing for {taxon_group.gbif_parent_species}.')
+ return HttpResponseRedirect(request.path_info)
+
harvest_session = HarvestSession.objects.create(
harvester=request.user,
start_time=datetime.now(),
@@ -127,7 +130,8 @@ def post(self, request, *args, **kwargs):
os.mkdir(log_file_folder)
with open(log_file_path, 'a+') as fi:
- harvest_session.log_file = File(fi, name=os.path.basename(fi.name))
+ harvest_session.log_file = File(
+ fi, name=os.path.basename(fi.name))
harvest_session.save()
harvest_gbif_species.delay(harvest_session.id)